WASHINGTON — The evacuation of 125 United States Special Operations advisers from Yemen in the past two days is the latest blow to the Obama administration’s counterterrorism campaign, which is already struggling with significant setbacks in Syria, Libya and elsewhere in the volatile region, American officials said Sunday.

The loss of Yemen as a base for American counterterrorism training, advising and intelligence-gathering carries major implications not just there, but throughout a region that officials say poses the most grievous threat to United States global interests and to the country itself.

The rapid rise of the Islamic State has commanded the immediate attention of President Obama and other Western leaders in the past year. But American officials say that Al Qaeda’s affiliate in Yemen, which includes the most potent bomb maker in the terrorist world, still poses the most direct threat to Americans at home, abroad or aboard commercial aircraft. Since 2009, the United States has thwarted at least three plots by the group to bring down airliners.

Even after the withdrawal of American troops, the Central Intelligence Agency will still maintain some covert Yemeni agents in the country. Armed drones will carry out some airstrikes from bases in nearby Saudi Arabia or Djibouti in the Horn of Africa, as was done most recently on Feb. 20. Spy satellites will still lurk overhead and eavesdropping planes will try to suck up electronic communications.

“We will have no intelligence footprint,” Representative Michael McCaul, a Texas Republican who is chairman of the House Homeland Security Committee, said Sunday on ABC’s “This Week.” “Good intelligence stops plots against the homeland. Without intelligence, we cannot effectively stop it.”

Other lawmakers, though, have expressed concern that the administration is exaggerating the terrorism threat, and warn that this could lead to further American military entanglements overseas.

But administration officials say that in many trouble spots they rely on allies — such as the French in West Africa to counter extremists like Boko Haram — rather than deploying large numbers of American troops.

Growing Instability in Yemen

In early 2014, Shiite insurgents known as Houthis consolidated control over Yemen’s Saada Province. In recent months, they have forced the Yemeni president out of office and expanded their influence south.

Controlled by Houthis

Houthis have influence or are able to operate

Areas where Al Qaeda is able to operate

SparSely populated

SAADA PROVINCE

YEMEN

Sana

SHABWA PROVINCE

Qaeda stronghold

Taiz

Aden

Houthi rebel fighters have taken control of parts of Taiz, Yemen’s third-largest city, including the international airport on Sunday.

The Houthis’s expansion puts them near Aden, where troops loyal to President Abdu Rabbu Mansour Hadi are based.

100 miles

200 miles

SparSely

populated

YEMEN

Sana

Taiz

Areas where Al Qaeda is able to operate.

Detail below

Controlled by Houthis

Houthis have influence or are able to operate

Areas where Al Qaeda is able to operate

SAADA PROVINCE

YEMEN

Sana

Taiz

SHABWA

PROVINCE

Qaeda

stronghold

Aden

Source: American Enterprise Institute's Critical Threats Project

MARCH 23, 2015

By The New York Times

The United States has worked around obstacles like Yemen’s turmoil before, notably in Pakistan and Somalia, where the C.I.A. and the Pentagon in the past decade stitched together local spy networks that provided information for drone strikes and occasional commando raids on Qaeda militants. But that approach has always been considered an imperfect substitute to having United States forces on the ground, training and advising military and security allies.

This challenge will also be a part of the discussions Mr. Obama and his top aides will hold with President Ashraf Ghani of Afghanistan this week.

About 2,000 of the approximately 10,000 troops that the United States is likely to carry over into 2016 — more than originally planned — are assigned to counterterrorism missions, mainly along the Afghan-Pakistan border. The C.I.A. relies on the American troops to provide security for its covert counterterrorism operations, including drone strikes in Pakistan.

What has complicated the American global counterterrorism mission most dramatically in the past year is the rise of the Islamic State, also known as ISIS or ISIL. The group’s expanding attraction now seems to be inspiring not only ideological followers from Nigeria to Afghanistan, but also loyalists with only tenuous ties to the parent group who are willing to carry out deadly attacks, as happened last week at a popular museum in Tunisia and two mosques in Yemen.

The Islamic State began attracting pledges of allegiance from groups and individual fighters after it declared the formation of a caliphate, or religious state, in June 2014. Counterterrorism analysts say it is using Al Qaeda’s franchise structure to expand its geographic reach, but without Al Qaeda’s rigorous, multiyear application process. This could allow its franchises to grow faster, easier and farther.

It is a trend that American counterterrorism officials say they are struggling to understand and defeat. Indeed, John O. Brennan, the C.I.A. director, voiced deep concerns this month over “the emergence of a terrorist threat that is increasingly decentralized, difficult to track and even more difficult to thwart.”

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With the Islamic State and its supporters producing as many as 90,000 Twitter posts and other social media responses every day, American officials also acknowledge the difficulty of blunting the group’s digital momentum in the same way a United States-led air campaign has slowed its advances on the battlefield in Iraq and, to a lesser extent, in Syria.

“We have an effective counternarrative, but the volume, the sheer volume, we are losing the battle today,” Michael B. Steinbach, the F.B.I.’s top counterterrorism official, told a House panel last month. “The amount of use of social media and other Internet-based activities eclipses our effort.”

Not only that, but after the disclosures by Edward J. Snowden, the former National Security Agency contractor, officials say it has become much harder for spy agencies to monitor what terrorists are saying and plotting, as militants have moved to couriers or communication networks the N.S.A. has yet to crack.

“We have less and less insight into terrorist planning because of the spread of encryption technology and the shrinking opportunity for human intelligence sources when it comes to troubled spots,” Nicholas J. Rasmussen, the director of the National Counterterrorism Center, said in a speech last month.

In Libya, at least three distinct groups have declared their affiliation with the Islamic State, one in each of the country’s component regions: Barqa in the east, Fezzan in the south, and Tripolitania in the west, around the capital. With fighting among other regional and ideological militias having already plunged the country into chaos, the Islamic State affiliates pose a new obstacle to Western attempts to negotiate a truce or a unity government.

“If I had to identify one of the greatest areas of emerging concern with respect to counterterrorism, it would be Libya,” Mr. Rasmussen told senators last month.

In Syria, the challenge is not only confronting the Islamic State, but also the Khorasan group. Khorasan is believed to be founded around fewer than two dozen senior Qaeda veterans who are ensconced in northwestern Syria, under the protection of Al Nusra, the Qaeda franchise there, developing plots against the West, American officials say.

And in Yemen, the American advisers who evacuated this weekend were initially able to sustain ties with regional Yemeni security forces and tribal leaders fighting Qaeda militants. That effort continued even after the American personnel relocated to a base in the south near Aden after the Houthi rebels ousted the government of President Abdu Rabbu Mansour Hadi, the Americans’ main partner.

But as Qaeda fighters seized a city 20 miles away from the base where the Americans were operating, administration officials opted to pull out the trainers.

Sunni extremists, including Islamic State fighters and Qaeda militants, have carried out deadly attacks against Shiite supporters of the Houthi rebel movement, which controls Sana and since September has been Yemen’s most dominant force.

The only silver lining to the collapsing security situation, some American officials say, is that Houthis are even more dedicated to fighting Al Qaeda than many of the Yemeni forces have been.

Still, Western officials and Yemeni experts fear that a security vacuum resembling Somalia’s would draw even more jihadists to ungoverned territory in Yemen, where they would have the space and time to plot attacks against the West.

“I don’t even think it’s accurate to think of Yemen as a single country anymore,” said Gregory D. Johnsen, a Yemen specialist and writer at large at BuzzFeed. “At best it has dissolved into a series of power blocs that are less and less able to influence change across the country.”

A version of this article appears in print on March 23, 2015, on Page A1 of the New York edition with the headline: Out of Yemen, U.S. Is Hobbled in Terror Fight. Order Reprints|Today's Paper|Subscribe